The game is kinda humor based, and in the comics I based this after, I state that it's the Hexagon, the cheap version of the Pentagon. And your goal is only to defend it if you play with the U.S., other then that, if you play with the satelite, SquidLO, or the aliens, you have to capture or destroy it.
The whole reason why it's the pentagon in this game is because there is no Hexagon tool (and it's nearly impossible to draw it with a brush) in flash. And the game won't be set i n the future, soley because it's based of the shooting down of the satelite they did 2 or 3 months ago.